SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q62255 from www.uniprot.org...

The NucPred score for your sequence is 0.66 (see score help below)

   1  MSRRKQAKPQHLKSDEELPPQDGASEHGVPGDGAEDADSGSESRSGSEET    50
  51  SVCEKCCAEFFKWADFLQHKKTCTKNPLVLIVHDDEPAPPSEDFPEPSPA   100
 101  SSPSDRTESEVAEEVAPTEGSEVKAATKEAEPMDVEVSTDKGPPGPSVPP   150
 151  PPPALPPQPEPAAFSMPSTNVTLETLLSTKVAVAQFSQGARAGGTTGAGG   200
 201  SVGAVAIPMILEQLVALQQQQIHQLQLIEQIRSQVALMSRQPGPPLKPSA   250
 251  SAPGTASVQLQGLTPHAALQLSAGPATASAGSGSTLPAAFDGPQHLSQPA   300
 301  SGTSTPCSTSAAPPDSGAHPACSTGPAPGAVAAASSTVGNAVQPQNASTP   350
 351  PALGPGPLLSSASNLPNPLLPQTSSSSVIFPNPLVSIAATANALDPLSAL   400
 401  MKHRKGKPPNVSVFEPKASAEDPFFKHKCRFCAKVFGSDSALQIHLRSHT   450
 451  GERPFKCNICGNRFSTKGNLKVHFQRHKEKYPHIQMNPYPVPEYLDNVPT   500
 501  CSGIPYGMSLPPEKPVTTWLDSKPVLPTVPTSVGLQLPPTVPGTHNYTDS   550
 551  PSITPVSRSPQRPSPASSECTSLSPGLNNTESGITVRPESPQPLLGGPSL   600
 601  TKAEPVSLPCTSTRTGDAPVVGGQVSGLPTSAATAVTDSACTSLGSPGLP   650
 651  AVSDQFKAQFPFGGLLDSMQTSETSKLQQLVENIDKKMTDPNQCVICHRV   700
 701  LSCQSALKMHYRTHTGERPFKCKICGRAFTTKGNLKTHFGVHRAKPPLRV   750
 751  QHSCPICQKKFTNAVVLQQHIRMHMGGQIPNTPLPEGLQEAMDADLPFDE   800
 801  KNAETLSSFDDDIDENSMEEDSELKDTASDSSKPLLSYSGSCPPSPPSVI   850
 851  SSIAALENQMKMIDSVMNCQQLANLKSVENGSGESDRLSNDSSSAVGDLE   900
 901  SRSAGSPALSESSSSQALSPAHSNGESFRSKSPGLGHQEDPQEIPLKTER   950
 951  LDSPPPGPGNGGALDLTAGHPGRPLIKEEAPFSLLFLSRERGKCASTVCG  1000
1001  VCGKPFACKSALEIHYRSHTKERRFVCTVCRRGCSTMGNLKQHLLTHKLK  1050
1051  ELPSQVFDPNFTLGPSHSTPSLASSPAPTMIKMEVNGHSKAIALGEGPAL  1100
1101  PAGVQVPTGPQTVMSPGLAPMLAPPPRRTPKQHNCQSCGKTFSSASALQI  1150
1151  HERTHTGEKPFGCTICGRAFTTKGNLKVHMGTHMWNNAPARRGRRLSVEN  1200
1201  PMALLGGDALKFSEMFQKDLAARAMNVDPSFWNQYAAAITNGLAMKNNEI  1250
1251  SVIQNGGIPQLPVSLGGGAIPPLGAMASGVDKARTGSSPPIVSLDKASSE  1300
1301  TGASRPFARFIEDNKEIGIN                                1320

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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